Figure 1

Analysis Schema. The left side of the figure shows a flow chart summarizing our methods. The right panels illustrate specific processes in the identification of a hemizygous deletion where one edge of the CNV is within targeted sequence. a) Targeted region with short reads aligned to the reference sequence, ratio of normalized coverage for sample versus lane median, and CNV call based on depth of coverage analysis. b) Sequence reads that align to the CNV edge shown in a). Black reads align across the complete 76 bp. Red reads are shorter segments of 76 bp reads that align perfectly to the region and indicate presence of mutation. c) Reads that partially-map to the CNV edge will also align to sequence flanking the other edge and can be used for exact breakpoint characterization, despite the one edge being in non-targeted sequence. The gap in the alignments represents the deleted sequence.